| "I once thought I could save the world... now look at it"
— Spoilers for Deus Ex: Mankind Divided follow!
Not much is known about how the organization was founded, but it appears some time after the events of Deus Ex: Human Revolution, the Illuminati looked for a new group to carry out their military operations after the Tyrants were all but wiped out and Belltower Associates went bankrupt (though later re-branding itself as Tarvos Security Services). It is possible the reason they did not turn to Tarvos is that the Illuminati decided they needed a group they could directly order and, while they were working to control or get rid of augmented people, they did prefer using them for operations, possibly because they had greater advantages in combat.
Whatever the reasons, by 2029 the Shadow Operatives had grown into a small army of well-armed augmented soldiers willing to perform clandestine activities without hesitation, even if it meant helping a cause that would ultimately hurt them as augmented individuals.